High throughput gene assembly in droplets

Abstract

Provided herein, among other things, is a method comprising: (a) obtaining a mixture of multiple sets of oligonucleotides, wherein the oligonucleotides within each set each comprise a terminal indexer sequence can be assembled to produce a synthon; and (b) hybridizing the oligonucleotide mixture to an array, thereby spatially-separating the different sets of oligonucleotides from one another. Other embodiments are also provided.

What is claimed is: 
     
         1 . A method comprising:
 (a) obtaining a mixture of multiple sets of oligonucleotides, wherein the oligonucleotides within each set each comprise a terminal indexer sequence and can be assembled to produce a synthon; and   (b) hybridizing the oligonucleotide mixture to an array, thereby spatially-separating the different sets of oligonucleotides from one another.   
     
     
         2 . The method of  claim 1 , wherein the oligonucleotides are single-stranded oligonucleotides. 
     
     
         3 . The method of  claim 1 , wherein the mixture comprises double-stranded oligonucleotides. 
     
     
         4 . The method of  claim 1 , wherein the oligonucleotides are single stranded and comprise a 3′ hairpin. 
     
     
         5 . The method of  claim 4 , comprising: contacting the array with a solution comprising a polymerase and nucleotides, thereby extending the hairpin and producing, for each feature bound by the oligonucleotides, a set of double-stranded extension products. 
     
     
         6 . The method of  claim 1 , wherein the oligonucleotides hybridize directly to oligonucleotides that are immobilized on the array. 
     
     
         7 . The method of  claim 1 , wherein the oligonucleotides hybridize via an adaptor to oligonucleotides that are immobilized on the array. 
     
     
         8 . The method of  claim 7 , wherein the method comprises: contacting the array with a solution comprising a polymerase and nucleotides, thereby extending the adaptor and producing, for each feature bound by the oligonucleotides, a set of double-stranded extension products. 
     
     
         9 . The method of  claim 1 , further comprising
 (c) contacting the array with a solution, thereby producing, for each feature bound by the oligonucleotides, a discrete droplet comprising one or more features.   
     
     
         10 . The method of  claim 9 , further comprising placing an immiscible liquid over the droplets, thereby producing, for each feature bound by the oligonucleotides, a discrete reaction chamber defined by a droplet. 
     
     
         11 . The method of  claim 10 , further comprising incubating the array under conditions by which a synthon is assembled in each of the reaction chambers. 
     
     
         12 . The method of  claim 11 , wherein the droplets comprise double-stranded oligonucleotides or double-stranded extension products, and the solution comprises a Type IIs restriction endonuclease, a DNA ligase and ATP, wherein the products of digestion of the double-stranded oligonucleotides or double-stranded extension products by the Type IIs restriction endonuclease are ligated to one another in a defined order by the DNA ligase in the discrete reaction chambers, thereby producing a synthon. 
     
     
         13 . The method of  claim 11 , wherein the oligonucleotides are single-stranded oligonucleotides and the method comprises:
 cleaving the terminal indexer sequence from the oligonucleotides to release assembly sequences from at least some of the oligonucleotides; and   assembling the synthon from the assembly sequences by polymerase chain assembly or by ligation.   
     
     
         14 . The method of  claim 13  wherein the cleaving the terminal indexer sequence from the oligonucleotide comprises cleaving a photocleavable linkage. 
     
     
         15 . The method of  claim 1 , wherein the oligonucleotides are double-stranded oligonucleotides that comprise staggered photocleavable or chemically cleavable linkages, and wherein the method comprises cleaving said staggered cleavable linkages using light or a chemical treatment to produce fragments that are ligatable to one another in order. 
     
     
         16 . The method of  claim 11 , further comprising separating the synthons from the array. 
     
     
         17 . A composition comprising multiple sets of oligonucleotides, wherein the oligonucleotides within each set comprise: (i) a terminal indexer sequence and (ii) an assembly sequence, wherein the terminal indexer sequence and the assembly sequence are separated by a photocleavable or chemically cleavable linker and the assembly sequences of each set of oligonucleotides can be assembled to produce a synthon. 
     
     
         18 . The composition of  claim 17 , wherein the assembly sequences of each set comprise overlapping complementary sequences that can be ligated directly to one another after cleavage of the terminal indexer sequences. 
     
     
         19 . The composition of  claim 17 , wherein the assembly sequences of each set comprise overlapping complementary sequences that can be assembled by polymerase chain assembly after cleavage of the terminal indexer sequences. 
     
     
         20 . An apparatus comprising:
 a planar support,   a plurality of spatially distinct droplets on a surface of the planar support, and   an immiscible liquid covering the droplets,   wherein the apparatus comprises a plurality of reaction chambers defined by the droplets, and each reaction chamber comprises a different synthon.